Running FCOM I've never actually had any problem with creature or NPC's bugging up, until I came across anything under the "Black Sun" faction, like the warriors and spellswords. During one of the Mages Guild quests I ran into a mess of these enemies in a ruin and... well, as you can see.

http://i118.photobucket.com/albums/o113/ZombieGenesis/Oblivion2011-04-2521-02-43-80.jpg

Sword faces, missing bodies, random protrusions. Doesn't make any sense.
Worse still, fighting these creatures results in CTD, killing them results in CTD, disabling with console leads to CTD...
I've tried re-arranging the WarCry plugin but I've had no luck. Is this a recognised issue?

I haven't seen this issue with playing Warcry for the longest time in my FCOM++ setup. Most probably an issue at your end.

Do you have Warcry v 1.09? Are you using BOSS, rebuilding your bashed patch etc.?